[Biojava-l] SimpleGapPenalty defaults

[Andreas Prlic]

Hi Kalil,

can you send your code snipplet that you are running? I just re-ran
the cookbook example and it works for me. Also this behaves fine:

ProteinSequence s1 = new
ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR");
		ProteinSequence s2 = new
ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR");
		
		SubstitutionMatrix<AminoAcidCompound> matrix = new
SimpleSubstitutionMatrix<AminoAcidCompound>();
		SequencePair<ProteinSequence, AminoAcidCompound> pair =
Alignments.getPairwiseAlignment(s1, s2,
				PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);
		System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(),
pair.getTarget().getAccession(), pair);
		
		System.out.println("Identicals:" + pair.getNumIdenticals());
		System.out.println("Similars:" + pair.getNumSimilars());

Andreas



On Wed, Jan 19, 2011 at 2:39 AM, Khalil El Mazouari
<khalil.elmazouari at gmail.com> wrote:
> Hi all,
>
> while doing PSA or MSA with default gop and gep values I obtained the following alignment!
>
> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA---------------------R
>
> Expected PSA should be at least
> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA-----R----------------
>
> this expected alignment was obtained with gop=1 and gep=100
>
> I can't understand while the PSA algorithm with default values always adds many gaps at the end of alignment to end up with a S:R while it is obvious that with less gaps we could obtain better SequencePair with R:R?
>
> Finally, how to get a score for PSA, that reflects the number of identical, similar residues and gaps?
>
> Many thanks.
>
> Khalil
>
>
>
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